From: The Economist, The Faith and Doubts of our Fathers (edited)
The founders of the USA didn't want people to fight about religion or have political disputes which were religious in their intensity.
They wanted to create a state run by a political system to which people with utterly different ideas could offer loyalty.
People who disagree over things they regard as ultimate usually can’t compromise. That's one reason for the separation of church and state.
Here is Jefferson on the topic:
“Let us reflect that, having banished from our land that religious intolerance under which mankind so long bled and suffered, we have yet gained little if we countenance a political intolerance as despotic, as wicked, and capable of as bitter and bloody persecutions.”